List<Test> getAlgorithms(Transaction t, TestType gssTT, boolean showAllAlgorithms) {
ViralIsolateFormConfig config =
RegaDBSettings.getInstance().getInstituteConfig().getViralIsolateFormConfig();
if (config.getAlgorithms() == null || showAllAlgorithms) {
return sortGSSTests(filterTests(t.getTests(), gssTT));
} else {
List<Test> tests = new ArrayList<Test>();
for (Algorithm a : config.getAlgorithms()) {
Test test =
t.getTest(a.getName(), gssTT.getDescription(), gssTT.getGenome().getOrganismName());
if (test != null && a.getOrganism().equals(gssTT.getGenome().getOrganismName()))
tests.add(test);
}
return filterTests(tests, gssTT);
}
}
public void init(Transaction t) {
filters_[0] = new StringFilter();
filters_[1] = new DateFilter(RegaDBSettings.getInstance().getDateFormat());
filters_[2] = new DateFilter(RegaDBSettings.getInstance().getDateFormat());
filters_[3] = new StringFilter();
}
public void loadTable(
Collection<String> drugClasses,
boolean showMutations,
boolean showAllAlgorithms,
Set<TestResult> testResults,
TestType gssTestType) {
clear();
if (gssTestType == null) {
return;
}
Transaction t = RegaDBMain.getApp().createTransaction();
List<DrugClass> sortedDrugClasses_ = t.getDrugClassesSortedOnResistanceRanking();
// drug names - column position
HashMap<String, Integer> algoColumn = new HashMap<String, Integer>();
int col = 0;
getElementAt(0, col).addWidget(new WText(""));
col = getColumnCount();
getElementAt(0, col).addWidget(new WText(""));
int maxWidth = 0;
for (Test test : getAlgorithms(t, gssTestType, showAllAlgorithms)) {
col = getColumnCount();
getElementAt(0, col).addWidget(new TableHeader(test.getDescription()));
getElementAt(0, col).setStyleClass("column-title");
algoColumn.put(test.getDescription(), col);
maxWidth += test.getDescription().length();
}
// drug names - row position
HashMap<String, Integer> drugColumn = new HashMap<String, Integer>();
List<DrugGeneric> genericDrugs;
int row;
boolean firstGenericDrugInThisClass;
for (DrugClass dc : sortedDrugClasses_) {
if (!drugClasses.contains(dc.getClassId())) continue;
genericDrugs = t.getDrugGenericSortedOnResistanceRanking(dc);
firstGenericDrugInThisClass = true;
for (DrugGeneric dg : genericDrugs) {
row = getRowCount();
if (firstGenericDrugInThisClass) {
getElementAt(row, 0).addWidget(new TableHeader(dc.getClassId() + ":"));
firstGenericDrugInThisClass = false;
getElementAt(row, 0).setStyleClass("form-label-area");
}
getElementAt(row, 1).addWidget(new TableHeader(dg.getGenericId()));
drugColumn.put(dg.getGenericId(), row);
getElementAt(row, 1).setStyleClass("form-label-area");
}
}
ViralIsolateFormConfig config =
RegaDBSettings.getInstance().getInstituteConfig().getViralIsolateFormConfig();
// clear table
for (int i = 1; i < getRowCount(); i++) {
for (int j = 2; j < getColumnCount(); j++) {
ViralIsolateFormUtils.putResistanceTableResult(
null, getElementAt(i, j), config, false, showMutations);
}
}
Integer colN;
Integer rowN;
for (TestResult tr : testResults) {
if (tr.getTest().getAnalysis() != null
&& Equals.isSameTestType(gssTestType, tr.getTest().getTestType())) {
if (!drugClasses.contains(tr.getDrugGeneric().getDrugClass().getClassId())) continue;
colN = algoColumn.get(tr.getTest().getDescription());
rowN = drugColumn.get(ViralIsolateFormUtils.getFixedGenericId(tr));
if (colN != null && rowN != null) {
ViralIsolateFormUtils.putResistanceTableResult(
tr, getElementAt(rowN, colN), config, false, showMutations);
}
}
}
}